Properties of bacterial endophytes and their proposed role in plant growth

Bacterial endophytes live inside plants for at least part of their life cycle. Studies of the interaction of endophytes with their host plants and their function within their hosts are important to address the ecological relevance of endophytes. The modulation of ethylene levels in plants by bacterially produced 1-aminocyclopropane-1-carboxylate deaminase is a key trait that enables interference with the physiology of the host plant. Endophytes with this capacity might profit from association with the plant, because colonization is enhanced. In turn, host plants benefit by stress reduction and increased root growth. This mechanism leads to the concept of 'competent' endophytes, defined as endophytes that are equipped with genes important for maintenance of plant-endophyte associations. The ecological role of these endophytes and their relevance for plant growth are discussed here.</p

PlantRNA_sniffer : a SVM-based workflow to predict long intergenic non-coding RNAs in plants

Non-coding RNAs (ncRNAs) constitute an important set of transcripts produced in the cells of organisms. Among them, there is a large amount of a particular class of long ncRNAs that are difficult to predict, the so-called long intergenic ncRNAs (lincRNAs), which might play essential roles in gene regulation and other cellular processes. Despite the importance of these lincRNAs, there is still a lack of biological knowledge and, currently, the few computational methods considered are so specific that they cannot be successfully applied to other species different from those that they have been originally designed to. Prediction of lncRNAs have been performed with machine learning techniques. Particularly, for lincRNA prediction, supervised learning methods have been explored in recent literature. As far as we know, there are no methods nor workflows specially designed to predict lincRNAs in plants. In this context, this work proposes a workflow to predict lincRNAs on plants, considering a workflow that includes known bioinformatics tools together with machine learning techniques, here a support vector machine (SVM). We discuss two case studies that allowed to identify novel lincRNAs, in sugarcane (Saccharum spp.) and in maize (Zea mays). From the results, we also could identify differentially-expressed lincRNAs in sugarcane and maize plants submitted to pathogenic and beneficial microorganisms

Dynamics of Seed-Borne Rice Endophytes on Early Plant Growth Stages

Bacterial endophytes are ubiquitous to virtually all terrestrial plants. With the increasing appreciation of studies that unravel the mutualistic interactions between plant and microbes, we increasingly value the beneficial functions of endophytes that improve plant growth and development. However, still little is known on the source of established endophytes as well as on how plants select specific microbial communities to establish associations. Here, we used cultivation-dependent and -independent approaches to assess the endophytic bacterrial community of surface-sterilized rice seeds, encompassing two consecutive rice generations. We isolated members of nine bacterial genera. In particular, organisms affiliated with Stenotrophomonas maltophilia and Ochrobactrum spp. were isolated from both seed generations. PCR-based denaturing gradient gel electrophoresis (PCR-DGGE) of seed-extracted DNA revealed that approximately 45% of the bacterial community from the first seed generation was found in the second generation as well. In addition, we set up a greenhouse experiment to investigate abiotic and biotic factors influencing the endophytic bacterial community structure. PCR-DGGE profiles performed with DNA extracted from different plant parts showed that soil type is a major effector of the bacterial endophytes. Rice plants cultivated in neutral-pH soil favoured the growth of seed-borne Pseudomonas oryzihabitans and Rhizobium radiobacter, whereas Enterobacter-like and Dyella ginsengisoli were dominant in plants cultivated in low-pH soil. The seed-borne Stenotrophomonas maltophilia was the only conspicuous bacterial endophyte found in plants cultivated in both soils. Several members of the endophytic community originating from seeds were observed in the rhizosphere and surrounding soils. Their impact on the soil community is further discussed

Properties of bacterial endophytes leading to maximized host fitness

Bacterial endophytes live inside plants for at least part of their life cycle. Studies of the interaction of endophytes with their host plants and their function within their hosts are important to examine the ecological relevance of endophytes. Plants appear to preferentially select beneficial bacteria to establish associations with them and to avoid detrimental microbes. The finding of particular compounds produced by the microbes and recognition proteins from the host has indicated the mechanisms involved in this selection. Furthermore, recent evidence shows that plants are even capable of applying a reward/sanction mechanism, allowing them to direct the selection of symbiosis, in terms of being optimal or less optimal. Here, we examine two mechanisms by which bacterial endophytes tinker with the metabolic pathways of their host plants, leading to enhanced fitness of both the host and the microorganism. Endophytes with the capacity to modulate plant ethylene levels by producing 1-aminocyclopropane-1-carboxylate (ACC) deaminase might ameliorate environmentally induced stress in the host plant. Concomitantly, the bacteria thus acquire their specific source of nutrients. The promotion of plant growth by the production of plant hormones leads to an increase in waste metabolites that are used by beneficial bacteria as growth substrates. These mechanisms lead to the concept of double-fitness enhancement and might explain how bacteria become 'competent' endophytes (Hardoim et al., 2008). The ecological role of these endophytes and their relevance for plant growth are discussed.</p

Properties of bacterial endophytes leading to maximized host fitness

Bacterial endophytes live inside plants for at least part of their life cycle. Studies of the interaction of endophytes with their host plants and their function within their hosts are important to examine the ecological relevance of endophytes. Plants appear to preferentially select beneficial bacteria to establish associations with them and to avoid detrimental microbes. The finding of particular compounds produced by the microbes and recognition proteins from the host has indicated the mechanisms involved in this selection. Furthermore, recent evidence shows that plants are even capable of applying a reward/sanction mechanism, allowing them to direct the selection of symbiosis, in terms of being optimal or less optimal. Here, we examine two mechanisms by which bacterial endophytes tinker with the metabolic pathways of their host plants, leading to enhanced fitness of both the host and the microorganism. Endophytes with the capacity to modulate plant ethylene levels by producing 1-aminocyclopropane-1-carboxylate (ACC) deaminase might ameliorate environmentally induced stress in the host plant. Concomitantly, the bacteria thus acquire their specific source of nutrients. The promotion of plant growth by the production of plant hormones leads to an increase in waste metabolites that are used by beneficial bacteria as growth substrates. These mechanisms lead to the concept of double-fitness enhancement and might explain how bacteria become 'competent' endophytes (Hardoim et al., 2008). The ecological role of these endophytes and their relevance for plant growth are discussed

Identification of isolated seed-borne strains.

a<p>Rice strains isolated from first (R1-R4) and second (R5-R16) generation of seeds.</p><p>*The 16S rRNA gene sequences of strains R6 and R8 were identical to PCR-DGGE products of the bands 12 and 9, respectively.</p>b<p>Source of the closest rice associated bacteria, LE – Leaf Endophyte <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Mano3" target="_blank">[21]</a>; LS – Leaf surface <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Mano3" target="_blank">[21]</a>; PF – Paddy Field (Islam et al., unpublished); PS – Paddy Soil <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Shrestha1" target="_blank">[28]</a>; R - Rhizosphere <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Steindler1" target="_blank">[25]</a>; RE1 - Root Endosphere <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Hardoim2" target="_blank">[20]</a>; RE2 - Root Endosphere <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Mano3" target="_blank">[21]</a> and SE – Seed endophyte <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Mano1" target="_blank">[5]</a>.</p

Biplot ordination diagrams of rice shoot and root bacterial endophytes.

<p>RDA diagrams generated from PCR-DGGE profiles of endophytic bacterial community sampled from shoot (A and B) and root (C and D) tissues of plants cultivated on K (A and C) and V (B and D) soils are shown. Squares and circle represent PCR-DGGE patterns of bacterial communities from plants submitted to, respectively, flooded and unflooded regimes and exposed to low- (empty symbol) and high- (full symbol) BID. Triangles (control treatment) represent PCR-DGGE patterns of bacterial communities from plants submitted to unflooded regime and cultivated in uninoculated soils. Six replicates of each treatment are shown. Stars represent nominal environmental variables. Arrows represent PCR-DGGE bands in which only the most descriptive communities are shown.</p

Heat map composition of selected bacterial communities.

<p>Distribution of select endophytic bacterial communities (rows) from two soil types (K and V) and four different habitats (root-free and rhizosphere soil, root and shoot endosphere) is shown. Cells are coloured in spectrum of grey that correlates with percentage of observed bacterium in a given habitat. Habitat from which the assessed bacterium was most likely to be originated from ‘artificial’ soil community is labelled with “inoculated”. Unlabelled cells are most likely represented by assessed bacterium originated from rice seeds.</p

Identification of excised PCR-DGGE bands.

a<p>Source of the closest rice associated bacteria: PF – Paddy Field <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Cuong1" target="_blank">[65]</a>; PS – Paddy Soil <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Shrestha1" target="_blank">[28]</a>; R - Rhizosphere <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Steindler1" target="_blank">[25]</a>; RE1 - Root Endosphere <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Hardoim2" target="_blank">[20]</a> and RE2 - Root Endosphere <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Sun1" target="_blank">[64]</a>.</p

Closest match of sequences obtained in this study against public available rice and <i>Zea</i> seed endophyte sequences.

<p>Closest match of sequences obtained in this study against public available rice and <i>Zea</i> seed endophyte sequences.</p